scholarly journals Proteomics Analyses of the Opportunistic PathogenBurkholderia vietnamiensisUsing Protein Fractionations and Mass Spectrometry

2011 ◽  
Vol 2011 ◽  
pp. 1-10 ◽  
Author(s):  
Samanthi Wickramasekara ◽  
Julie Neilson ◽  
Naren Patel ◽  
Linda Breci ◽  
Amy Hilderbrand ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Tandem Mass Spectrometry ◽  
Virulence Factors ◽  
Protein Identification ◽  
Reversed Phase ◽  
Tandem Mass ◽  
Burkholderia Vietnamiensis ◽  
Ms Analysis ◽  
Liquid Chromatography Tandem Mass ◽  
Identification Technique

The main objectives of this work were to obtain a more extensive coverage of theBurkholderia vietnamiensisproteome than previously reported and to identify virulence factors using tandem mass spectrometry. The proteome ofB. vietnamiensiswas precipitated into four fractions to as extracellular, intracellular, cell surface and cell wall proteins. Two different approaches were used to analyze the proteins. The first was a gel-based method where 1D SDS-PAGE was used for separation of the proteins prior to reverse phase liquid chromatography tandem mass spectrometry (LC-MS/MS). The second method used MudPIT analysis (Multi dimensional Protein Identification Technique), where proteins are digested and separated using cation exchange and reversed phase separations before the MS/MS analysis (LC/LC-MS/MS). Overall, gel-based LC-MS/MS analysis resulted in more protein identifications than the MudPIT analysis. Combination of the results lead to identification of more than 1200 proteins, approximately 16% of the proteins coded from the annotated genome ofBurkholderiaspecies. Several virulence factors were detected including flagellin, porin, peroxiredoxin and zinc proteases.

scholarly journals Validation of Liquid Chromatography–Tandem Mass Spectrometry Method for Analysis of Urinary Conjugated Metanephrine and Normetanephrine for Screening of Pheochromocytoma

2002 ◽  
Vol 48 (3) ◽  
pp. 533-539 ◽  
Author(s):  
Robert L Taylor ◽  
Ravinder J Singh
Keyword(s):  
Mass Spectrometry ◽  
Liquid Chromatography ◽  
Tandem Mass Spectrometry ◽  
Solid Phase ◽  
Reversed Phase ◽  
Selected Reaction Monitoring ◽  
Gas Chromatography Mass Spectrometry ◽  
Tandem Mass ◽  
Chromatography Tandem Mass Spectrometry ◽  
Liquid Chromatography Tandem Mass

Abstract Background: Metanephrines are biochemical markers for tumors of the adrenal medulla (e.g., pheochromocytoma) and other tumors derived from neural crest cells (e.g., paragangliomas and neuroblastomas). We describe a liquid chromatography–tandem mass spectrometry (LC-MS/MS) method for the measurement of urinary conjugated metanephrines. Methods: We added 250 ng of d3-metanephrine (d3-MN) and 500 ng of d3-normetanephrine (d3-NMN) to 1 mL of urine samples as stable isotope internal standards. The samples were then acidified, hydrolyzed for 20 min in a 100 °C water bath, neutralized, and prepared by solid-phase extraction. The methanol eluates were analyzed by LC-MS/MS in the selected-reaction-monitoring mode after separation on a reversed-phase amide C16 column. Results: Multiple calibration curves for the analysis of urine MN and NMN exhibited consistent linearity and reproducibility in the range of 10–5000 μg/L. Interassay CVs were 5.7–8.6% at mean concentrations of 90–4854 μg/L for MN and NMN. The detection limit was 10 μg/L. Recovery of MN and NMN (144–2300 μg/L) added to urine was 91–114%. The regression equation for the LC-MS/MS (x) and colorimetric (y) methods was: y = 0.81x − 0.006 (r = 0.822; n = 110). The equation for the HPLC (x) and LC-MS/MS (y) methods was: y = 1.09x + 0.05 (r = 0.998; n = 40). Conclusions: The sensitivity and specificity of the MS/MS method for urinary conjugated metanephrines offer advantages over colorimetric, immunoassay, HPLC, and gas chromatography–mass spectrometry methods because of elimination of drug interferences, high throughput, and short chromatographic run time.

scholarly journals PATH-19. TUMOR HETEROGENEITY IN GLIOMAS: A PILOT STUDY OF HISTOPATHOLOGY-ASSOCIATED PROTEOME PROFILES ASSESSED BY LIQUID CHROMATOGRAPHY TANDEM MASS SPECTROMETRY OF FFPE SAMPLES

2019 ◽  
Vol 21 (Supplement_6) ◽  
pp. vi147-vi147
Author(s):  
Aline Paixao Becker ◽  
Erica Hlavin Bell ◽  
S Jaharul Haque ◽  
Joseph McElroy ◽  
Jessica Fleming ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Liquid Chromatography ◽  
Tandem Mass Spectrometry ◽  
Tumor Heterogeneity ◽  
High Expression ◽  
Tandem Mass ◽  
Chromatography Tandem Mass Spectrometry ◽  
Ms Analysis ◽  
Ffpe Samples ◽  
Liquid Chromatography Tandem Mass

Abstract Herein, we aimed to scrutinize tumor heterogeneity of infiltrative gliomas based on histopathological phenotypes, through proteomic profiling of formalin-fixed, paraffin embedded (FFPE) tissue. FFPE tissues are promising samples for proteomic studies, which can support the elucidation of glioma evolution and identify therapeutically vulnerable proteins and signaling pathways that drive recurrence and resistance mechanisms. We represented 2–3 adjacent, phenotypically distinct areas from 12 grade II-IV gliomas diagnosed according to the 2016 WHO classification, in a total of 35 samples (1.0mm cores), that were analyzed employing liquid chromatography tandem mass spectrometry (LC-MS/MS) for label-free expression proteomics. The statistical analysis was performed using R and Qlucore™ omics explorer software. Overall, 9222 peptides were mapped to 1758 non-redundant proteins, 320 of which had a significant (p< 0.05) differential expression in glioblastomas versus lower grade gliomas (Wilcoxon test comparing average expression). Principal component analysis (PCA) of the whole set of proteins showed clustering of the samples by tumor grade and IDH status. Unsupervised hierarchical analysis of the most significantly expressed proteins (p= 0.01, FDR= 0.05) showed that IDHwt gliomas had high expression of proteins related to cell movement, DNA structure, and fatty acid metabolism throughout the samples. IDHmut gliomas largely displayed high expression of mitochondrial enzymes related to energy production and neurotransmitter metabolism, with subsets closely related to 1p19q status and histological grade. Importantly, we demonstrated that LC-MS/MS analysis of FFPE core samples is feasible and enables recognition of different proteome signatures across histopathological phenotypes within a single tumor. This is the first study, to our knowledge, exploring proteome profiles addressing histopathological heterogeneity in gliomas by LC-MS/MS analysis of FFPE samples, which warrants further validation in independent datasets including ones that utilize frozen specimens. FUNDING: R01CA108633, R01CA169368, RC2CA148190, U10CA180850-01 (NCI), Brain Tumor Funders Collaborative Grant, and the Ohio State University CCC (all to AC).

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